Merge pull request #194 from weecology/sfwbr

South Florida Wading Bird Report tables and figures [no version bump]

Author: gmyenni

Reports/sfwbr_recovery_report.R

@@ -0,0 +1,89 @@
+library(tidyr)
+library(dplyr)
+library(wader)
+library(ggplot2)
+library(rJava)
+library(xlsx)
+
+report_year = 2024
+
+wb <- createWorkbook()
+#--------------------
+# DEFINE CELL STYLES
+#--------------------
+# title and subtitle styles
+title_style <- CellStyle(wb) +
+  Font(wb, heightInPoints = 12,
+       name="Calibri",
+       underline = 1)
+
+subtitle_style <- CellStyle(wb) +
+  Font(wb,
+       name="Calibri",
+       heightInPoints = 10)
+
+# data table styles
+cs <- CellStyle(wb) +
+  Font(wb, heightInPoints=11, name="Calibri") +
+  Alignment(horizontal = "ALIGN_CENTER")
+
+rowname_style <- CellStyle(wb)  +
+  Font(wb, name = "Calibri") +
+  Alignment(horizontal = "ALIGN_CENTER") +
+  Border(position = c("RIGHT"),
+         pen = c("BORDER_THIN"))
+
+colname_style <- CellStyle(wb) +
+  Font(wb, name = "Calibri") +
+  Alignment(horizontal = "ALIGN_CENTER") +
+  Border(position = c("TOP", "BOTTOM"),
+         pen = c("BORDER_THIN"))
+
+xlsx.addTitle <- function(sheet, rowIndex, title, titleStyle) {
+  rows <- createRow(sheet, rowIndex = rowIndex)
+  sheetTitle <- createCell(rows, colIndex = 1)
+  setCellValue(sheetTitle[[1,1]], title)
+  setCellStyle(sheetTitle[[1,1]], titleStyle)
+}
+
+#### Get data ###
+
+indicator_data <- max_count_indicator(maxyear = report_year) %>%
+  filter(species %in% c("greg","sneg","whib","wost")) %>%
+  pivot_wider(id_cols = year, names_from = species, values_from = count_mean) %>%
+  mutate(across(2:5, \(x) round(x, 0))) %>%
+  rename_with(toupper, .cols = -year)
+
+#--------------------
+# BUILD WORKBOOK
+#--------------------
+
+#### Build WCAS sheet ####
+maxcount <- createSheet(wb, sheetName = "Max Count")
+
+xlsx.addTitle(sheet = maxcount, rowIndex = 1,
+              title = paste("Three-year running averages of numbers of nesting pairs of Great Egrets, Snowy Egrets, White Ibises, and Wood Storks in the mainland Everglades (WCAs + ENP, not including Florida Bay) in ", report_year,".", sep=""),
+              titleStyle = title_style)
+
+addDataFrame(indicator_data, sheet = maxcount, startRow = 3, startColumn = 1,
+             colnamesStyle = colname_style, colStyle = cs,
+             rownamesStyle = rowname_style)
+
+#### Write ####
+saveWorkbook(wb, file = 'Reports/recovery_report_table_2024.xlsx')
+
+
+### Write figures ####
+
+# Do max count plot in Excel
+# max_count_plot(maxyear = report_year)
+# ggsave("my_plot.png", plot = my_plot, width = 6, height = 4, units = "in", dpi = 300)
+
+coastal <- plot_coastal(maxyear = report_year)
+ggsave("coastal.png", plot = coastal, width = 6, height = 4, units = "in", dpi = 300)
+foraging <- plot_foraging(maxyear = report_year)
+ggsave("foraging.png", plot = foraging, width = 6, height = 4, units = "in", dpi = 300)
+initiation <- plot_initiation(maxyear = report_year)
+ggsave("initiation.png", plot = initiation, width = 6, height = 4, units = "in", dpi = 300)
+supercolony <- plot_supercolony(maxyear = report_year)
+ggsave("supercolony.png", plot = supercolony, width = 6, height = 4, units = "in", dpi = 300)